# 0.6 Dimensionality reduction methods for molecular motion  (Page 9/13)

 Page 9 / 13

Applying the PCA procedure as outlined before to a set of HIV-1 samples from simulation produces 1,782-dimensional principal components. Since the physical interpretation of the PCs is quite intuitive in this case, the PC coordinates can be split in groups of 3 to obtain the $\mathrm{\left(x,y,z\right)}$ components for each of the 594 atoms. These components are 3-dimensional vectors that point in the direction each atom would follow along the first PC. In figure 6 a), the per-atom components of the first PC have been superimposed in purple.

Figure 6 b) shows the effect of interpolating HIV-1 conformations along the first PC, or first mode of motion. Starting from an aligned conformation from the original data set, multiples of the first PC can be added to produce interpolated conformations. Note that the first mode of motion corresponds mostly to the "opening" and "closing" of the flaps, as can be inferred from the relative magnitued of the first PC components in the flap region. Thus, interpolating in the direction of the first PC produces an approximation of this motion, but using only one degree of freedom. This way, the complex dynamics of the system and the 1,782 apparent degrees of freedom have been approximated by just one, effectively reducing the dimensionality of the representation.

Figure 7 (solid line) shows the residual variance left unexplained by discarding the lower-ranked principal components. Residual variance plots always decrease, and in this case, the first PC accounts for approximately 40% of the total variance along the motion (the dashed line shows the percentage of total variance explained up to the given PC). Also, the first 10 PCs account for more than 70% of the total data variance. Given the dominance of only a few degrees of freedom it is possible to represent the flexibility of the protein in a drastically reduced search space.

## Non-linear methods

PCA falls in the category of what is called a linear method, since mathematically, the PCs are computed as a series of linear operations on the input coordinates. Linear methods such as PCA work well only when the collective atom motions are small (or linear), which is hardly the case for most interesting biological processes. Non-linear dimensionality reduction methods do exist, but are normally much more computationally expensive and have other disadvantages as well. However, non-linear methods are much more effective in describing complex processes using much fewer parameters.

how to know photocatalytic properties of tio2 nanoparticles...what to do now
it is a goid question and i want to know the answer as well
Maciej
Do somebody tell me a best nano engineering book for beginners?
what is fullerene does it is used to make bukky balls
are you nano engineer ?
s.
fullerene is a bucky ball aka Carbon 60 molecule. It was name by the architect Fuller. He design the geodesic dome. it resembles a soccer ball.
Tarell
what is the actual application of fullerenes nowadays?
Damian
That is a great question Damian. best way to answer that question is to Google it. there are hundreds of applications for buck minister fullerenes, from medical to aerospace. you can also find plenty of research papers that will give you great detail on the potential applications of fullerenes.
Tarell
what is the Synthesis, properties,and applications of carbon nano chemistry
Mostly, they use nano carbon for electronics and for materials to be strengthened.
Virgil
is Bucky paper clear?
CYNTHIA
so some one know about replacing silicon atom with phosphorous in semiconductors device?
Yeah, it is a pain to say the least. You basically have to heat the substarte up to around 1000 degrees celcius then pass phosphene gas over top of it, which is explosive and toxic by the way, under very low pressure.
Harper
Do you know which machine is used to that process?
s.
how to fabricate graphene ink ?
for screen printed electrodes ?
SUYASH
What is lattice structure?
of graphene you mean?
Ebrahim
or in general
Ebrahim
in general
s.
Graphene has a hexagonal structure
tahir
On having this app for quite a bit time, Haven't realised there's a chat room in it.
Cied
what is biological synthesis of nanoparticles
what's the easiest and fastest way to the synthesize AgNP?
China
Cied
types of nano material
I start with an easy one. carbon nanotubes woven into a long filament like a string
Porter
many many of nanotubes
Porter
what is the k.e before it land
Yasmin
what is the function of carbon nanotubes?
Cesar
I'm interested in nanotube
Uday
what is nanomaterials​ and their applications of sensors.
what is nano technology
what is system testing?
preparation of nanomaterial
Yes, Nanotechnology has a very fast field of applications and their is always something new to do with it...
what is system testing
what is the application of nanotechnology?
Stotaw
In this morden time nanotechnology used in many field . 1-Electronics-manufacturad IC ,RAM,MRAM,solar panel etc 2-Helth and Medical-Nanomedicine,Drug Dilivery for cancer treatment etc 3- Atomobile -MEMS, Coating on car etc. and may other field for details you can check at Google
Azam
anybody can imagine what will be happen after 100 years from now in nano tech world
Prasenjit
after 100 year this will be not nanotechnology maybe this technology name will be change . maybe aftet 100 year . we work on electron lable practically about its properties and behaviour by the different instruments
Azam
name doesn't matter , whatever it will be change... I'm taking about effect on circumstances of the microscopic world
Prasenjit
how hard could it be to apply nanotechnology against viral infections such HIV or Ebola?
Damian
silver nanoparticles could handle the job?
Damian
not now but maybe in future only AgNP maybe any other nanomaterials
Azam
Hello
Uday
I'm interested in Nanotube
Uday
this technology will not going on for the long time , so I'm thinking about femtotechnology 10^-15
Prasenjit
can nanotechnology change the direction of the face of the world
how did you get the value of 2000N.What calculations are needed to arrive at it
Privacy Information Security Software Version 1.1a
Good
Got questions? Join the online conversation and get instant answers!